Hi Gabriel,
Have you tried mri_label2vol?
If you want the volume in the anatomical space:
mri_label2vol --label labelname.label --temp <T1_template>.nii.gz --identity --o volumename.nii.gz
If you want it in some other space, you can specify the registration matrix using --reg and the template using --temp.
Hope that helps, Priti
<div style="font-family: 'Times New Roman'; font-size: 16px; "><div>Hello FreeSurfers,</div><div><br /></div><div>Does any one of you know if exist a function to export labels as a ROI format?</div><div><br /></div><div>Regards,</div><div>Gabriel</div></div><div><br />-- <br /></div><div><font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font></div> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't think so. What is .roi format?
On 04/24/2012 12:21 PM, Gabriel Gonzalez Escamilla wrote:
Thanks Priti,
I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?
Regards, Gabriel
El 24/04/12, *Priti Srinivasan * rspriti@nmr.mgh.harvard.edu escribió:
Hi Gabriel,
Have you tried mri_label2vol?
If you want the volume in the anatomical space:
mri_label2vol --label labelname.label --temp <T1_template>.nii.gz --identity --o volumename.nii.gz
If you want it in some other space, you can specify the registration matrix using --reg and the template using --temp.
Hope that helps, Priti
<div style="font-family: 'Times New Roman'; font-size: 16px;
"><div>Hello
FreeSurfers,</div><div><br /></div><div>Does any one of you know if
exist
a function to export labels as a ROI format?</div><div><br /></div><div>Regards,</div><div>Gabriel</div></div><div><br />-- <br /></div><div><font size="3">--------------------------<br />PhD.
student
Gabriel González-Escamilla<br />Laboratory of Functional
Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font></div> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
they are just ascii files so it should be easy enough to do yourself On Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote:
Thanks Priti,
I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS?
Regards, Gabriel
El 24/04/12, Priti Srinivasan rspriti@nmr.mgh.harvard.edu escribió: Hi Gabriel,
Have you tried mri_label2vol? If you want the volume in the anatomical space: mri_label2vol --label labelname.label --temp <T1_template>.nii.gz --identity --o volumename.nii.gz If you want it in some other space, you can specify the registration matrix using --reg and the template using --temp. Hope that helps, Priti > <div style="font-family: 'Times New Roman'; font-size: 16px; "><div>Hello > FreeSurfers,</div><div><br /></div><div>Does any one of you know if exist > a function to export labels as a ROI format?</div><div><br > /></div><div>Regards,</div><div>Gabriel</div></div><div><br />-- <br > /></div><div><font size="3">--------------------------<br />PhD. student > Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br > />Department of Physiology, Anatomy, and Cell Biology<br />University > Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- > Spain -<br /><br />Email: ggonesc@upo.es<br > />http://www.upo.es/neuroaging/es/</font></div> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
sorry, I don't know what obj format is either Bruce On Wed, 25 Apr 2012, Gabriel Gonzalez Escamilla wrote:
And what about exporting as obj format, I have found a function to transform surfaces to obj, is it possible something like this but with the labels? Regards, Gabriel
El 24/04/12, Bruce Fischl fischl@nmr.mgh.harvard.edu escribió: they are just ascii files so it should be easy enough to do yourself On Tue, 24 Apr 2012, Gabriel Gonzalez Escamilla wrote:
>Thanks Priti, > >I've thought about that before, but actually I'm looking for literally .roi images, do you know if is this format possible from FS? > >Regards, >Gabriel > > > >El 24/04/12, Priti Srinivasan <rspriti@nmr.mgh.harvard.edu> escribió: > Hi Gabriel, > > Have you tried mri_label2vol? > > If you want the volume in the anatomical space: > > mri_label2vol --label labelname.label --temp <T1_template>.nii.gz > --identity --o volumename.nii.gz > > If you want it in some other space, you can specify the registration > matrix using --reg and the template using --temp. > > Hope that helps, > Priti > > > > > <div style="font-family: 'Times New Roman'; font-size: 16px; "><div>Hello > > FreeSurfers,</div><div><br /></div><div>Does any one of you know if exist > > a function to export labels as a ROI format?</div><div><br > > /></div><div>Regards,</div><div>Gabriel</div></div><div><br />-- <br > > /></div><div><font size="3">--------------------------<br />PhD. student > > Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br > > />Department of Physiology, Anatomy, and Cell Biology<br />University > > Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- > > Spain -<br /><br />Email: ggonesc@upo.es<br > > />http://www.upo.es/neuroaging/es/</font></div> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > >-- >-------------------------- >PhD. student Gabriel González-Escamilla >Laboratory of Functional Neuroscience >Department of Physiology, Anatomy, and Cell Biology >University Pablo de Olavide >Ctra. de Utrera, Km.1 >41013 - Seville >- Spain - > >Email: ggonesc@upo.es >http://www.upo.es/neuroaging/es/ > >--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Gabriel Gonzalez Escamilla -
Priti Srinivasan